I have something to add to the "Flood as a Doomsday Weapon" theory. Sure, the Forerunners could have just wiped people out with the Halos, but why make it quick and painless, when you can make your enemies suffer, and use them as an example to other species.

Sounds great. I just get nervous around the part when the Flood get out of control and start "making an example" out of me :